Perhaps you could make a one page ePub which demonstrates the problem, with screen shots showing how your reading displays margins without padding specified and then with padding specified. I'm just wondering if a bit more context may help give some insight into what's going on here - hence posting a full ePub rather than just code snippets.
I'm still surprised that any reader would mess up the margin style simply because of the presence of padding.
(You can generate some random paragraph text from
http://www.lipsum.com/)